Fig. 4: RNA-seq demonstrates the regulatory mechanism underlying nlrc3 in HSPC emergence. | Nature Communications

Fig. 4: RNA-seq demonstrates the regulatory mechanism underlying nlrc3 in HSPC emergence.

From: Nlrc3 signaling is indispensable for hematopoietic stem cell emergence via Notch signaling in vertebrates

Fig. 4: RNA-seq demonstrates the regulatory mechanism underlying nlrc3 in HSPC emergence.The alternative text for this image may have been generated using AI.

a Schematic representation of RNA-seq analysis in this study. b Principal-component analysis (PCA) of six sequenced samples shown by the first three principal components (PC1–PC2). Control MO 1, blue; Control MO 2, light blue; Control MO 3, violet; nlrc3 MO 1, yellow; nlrc3 MO 2, green; nlrc3 MO 3, red; c Heatmap showing differential expression of hematologic-associated genes. The mark * indicates that there is a significant difference between the control group and morphant group with fold change >2 or fold change <0.5 and p-value < 0.05. (4) FDR < 0.05. d Representative statistically enriched biological process (BP), molecular function (MF) and cellular component (CC) associated genes of the upregulated and downregulated genes in nlrc3 morphant group compared with the control group. e Representative KEGG enrichment scatter plots of the signaling pathways in the nlrc3 morphant group compared with the control group. The plots were drawn based on the R version 4.1.3 and ggplot version 3.3.3. The statistical tests were one-sided and adjustments were made for multiple comparisons. f Expression of Notch genes in control embryos and nlrc3 morphants at 26 hpf by RNA-seq. Error bars, mean ± s.d., ns = 0.0554, 0.0645, 0.1207, *P = 0.0224, **P = 0.0065, 0.0029, 0.0066, ***P = 0.0006, 0.0004, ****P < 0.0001, the exact p-values mentioned above are listed from left to right, by using two-tailed, unpaired Student’s t-test. n = 3 biological replicates. g Enrichment plot of the hematopoietic cell lineages between differentially regulated genes in the nlrc3 morphant group compared with the control group by GSEA (Gene Set Enrichment Analysis). P = 0.0465. h Enrichment plot of the Notch signaling pathway between differentially regulated genes in the nlrc3 morphant group compared with the control group by GSEA. P = 0.0003. GSEA of nlrc3 morphant versus control group transcriptional profiles using software GSEA (v4.1.0) and MSigDB, the statistical tests were one-sided and adjustments were made for multiple comparisons. Black bars indicate the individual genes, enrichment is in green. Normalized enrichment score = NES in (g, h). Source data are provided as a Source Data file.

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